pipelines.chromake.scripts.paths
pipelines.chromake.scripts.paths
The paths module of chromake contains functions to identify the inputs and the files generated by the chromake pipeline.
Functions
| Name | Description |
|---|---|
| get_all_sequencings_related_paths | Get the path to the files generated by the pipeline for the samples of all sequencings and projects. |
| get_project_paths_for_macs3 | Get a dictionary with the files necessary for the macs3 rules of a project. |
| get_sequencings_related_paths | Get the path to the files generated by the pipeline for the samples of a specific sequencing. |
get_project_paths_for_macs3
pipelines.chromake.scripts.paths.get_project_paths_for_macs3(
cfg,
project_name,
mode,
)Get a dictionary with the files necessary for the macs3 rules of a project.
Parameters
| Name | Type | Description | Default |
|---|---|---|---|
| cfg | dict | Dict representing the configuration of an analysis with the chromake pipeline. | required |
| project_name | str | String representing the name of the project in cfg | required |
| mode | str | String indicating the output. Accepted values are: - macs3 (dict with all inputs and the outputs of the macs3 command for all samples associated with the project) - macs3_output (list of all outputs of the macs3 command for the project) | required |
Returns
| Name | Type | Description |
|---|---|---|
| A dictionary of all file paths for the project. |